Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: V5731

Calculation Name: 2HLC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HLC

Chain ID: A

ChEMBL ID:

UniProt ID: P08897

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2866212.230016
FMO2-HF: Nuclear repulsion 2777219.900803
FMO2-HF: Total energy -88992.329213
FMO2-MP2: Total energy -89251.13506


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:16:ILE)


Summations of interaction energy for fragment #1(A:16:ILE)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-29.981-21.36937.92-16.544-29.991-0.123
Interaction energy analysis for fragmet #1(A:16:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.067 / q_NPA : -0.050
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A18ASN0-0.075-0.0543.051-0.0541.9860.223-0.949-1.314-0.001
4A19GLY00.0310.0132.538-0.3180.4871.097-0.778-1.123-0.001
5A20TYR0-0.090-0.0323.150-0.048-0.7580.0890.866-0.2470.000
6A21GLU-1-0.807-0.8895.6140.7030.7030.0000.0000.0000.000
7A22ALA0-0.025-0.0137.191-0.074-0.0740.0000.0000.0000.000
8A23TYR00.0030.0028.800-0.045-0.0450.0000.0000.0000.000
9A24THR00.012-0.01512.0440.0250.0250.0000.0000.0000.000
10A25GLY00.0820.04013.864-0.012-0.0120.0000.0000.0000.000
11A26LEU0-0.101-0.0159.518-0.007-0.0070.0000.0000.0000.000
12A27PHE00.004-0.0137.1480.0270.0270.0000.0000.0000.000
13A28PRO00.0090.00711.204-0.030-0.0300.0000.0000.0000.000
14A29TYR00.0620.0408.975-0.045-0.0450.0000.0000.0000.000
15A30GLN0-0.028-0.0056.4650.0500.0500.0000.0000.0000.000
16A31ALA00.0060.00010.298-0.006-0.0060.0000.0000.0000.000
17A32GLY00.0400.01610.015-0.048-0.0480.0000.0000.0000.000
18A33LEU0-0.071-0.03211.5250.0500.0500.0000.0000.0000.000
19A34ASP-1-0.725-0.83313.080-0.222-0.2220.0000.0000.0000.000
20A35ILE0-0.010-0.00813.8530.0420.0420.0000.0000.0000.000
21A36THR0-0.0080.00717.122-0.014-0.0140.0000.0000.0000.000
22A37LEU00.0070.00717.7500.0130.0130.0000.0000.0000.000
23A37GLN00.014-0.00821.2880.0140.0140.0000.0000.0000.000
24A37ASP-1-0.874-0.91621.910-0.190-0.1900.0000.0000.0000.000
25A37GLN0-0.064-0.04323.808-0.001-0.0010.0000.0000.0000.000
26A38ARG10.8440.92318.7360.2420.2420.0000.0000.0000.000
27A39ARG10.8260.87516.2270.1700.1700.0000.0000.0000.000
28A40VAL0-0.002-0.00512.755-0.037-0.0370.0000.0000.0000.000
29A41TRP00.0110.0187.7890.1380.1380.0000.0000.0000.000
30A42CYS0-0.089-0.0219.204-0.174-0.1740.0000.0000.0000.000
31A43GLY00.0730.0477.5850.0710.0710.0000.0000.0000.000
32A44GLY00.0220.0008.6260.0150.0150.0000.0000.0000.000
33A45SER0-0.0170.00210.1150.0630.0630.0000.0000.0000.000
34A46LEU00.0000.01012.137-0.026-0.0260.0000.0000.0000.000
35A47ILE0-0.021-0.02115.4750.0220.0220.0000.0000.0000.000
36A48ASP-1-0.789-0.91617.7700.0380.0380.0000.0000.0000.000
37A49ASN0-0.044-0.01220.352-0.003-0.0030.0000.0000.0000.000
38A50LYS10.8070.91522.671-0.035-0.0350.0000.0000.0000.000
39A51TRP00.0020.00020.209-0.015-0.0150.0000.0000.0000.000
40A52ILE00.0350.03014.2210.0140.0140.0000.0000.0000.000
41A53LEU0-0.032-0.00814.513-0.012-0.0120.0000.0000.0000.000
42A54THR00.014-0.01711.702-0.005-0.0050.0000.0000.0000.000
43A55ALA00.0430.02612.0490.0320.0320.0000.0000.0000.000
44A56ALA0-0.021-0.01313.863-0.014-0.0140.0000.0000.0000.000
45A57HIS0-0.067-0.05511.342-0.093-0.0930.0000.0000.0000.000
46A59VAL00.005-0.02214.8950.0090.0090.0000.0000.0000.000
47A59HIS0-0.0370.00218.2810.0390.0390.0000.0000.0000.000
48A60ASP-1-0.880-0.94219.934-0.183-0.1830.0000.0000.0000.000
49A61ALA0-0.015-0.01019.331-0.004-0.0040.0000.0000.0000.000
50A62VAL0-0.078-0.02721.3220.0170.0170.0000.0000.0000.000
51A63SER0-0.031-0.03122.2790.0160.0160.0000.0000.0000.000
52A64VAL00.005-0.00516.851-0.018-0.0180.0000.0000.0000.000
53A65VAL0-0.0180.00718.4380.0210.0210.0000.0000.0000.000
54A66VAL0-0.010-0.02015.627-0.020-0.0200.0000.0000.0000.000
55A67TYR0-0.039-0.01013.9320.0180.0180.0000.0000.0000.000
56A68LEU00.0470.00514.1550.0020.0020.0000.0000.0000.000
57A69GLY00.0790.02815.020-0.006-0.0060.0000.0000.0000.000
58A70SER0-0.017-0.00914.0510.0150.0150.0000.0000.0000.000
59A71ALA00.0180.01210.100-0.007-0.0070.0000.0000.0000.000
60A72VAL0-0.0110.0119.9890.0710.0710.0000.0000.0000.000
61A73GLN00.0140.0049.2680.0260.0260.0000.0000.0000.000
62A74TYR0-0.086-0.04611.609-0.030-0.0300.0000.0000.0000.000
63A75GLU-1-0.897-0.94614.4380.0790.0790.0000.0000.0000.000
64A76GLY0-0.022-0.03315.1570.0060.0060.0000.0000.0000.000
65A80GLU-1-0.891-0.89417.3990.0950.0950.0000.0000.0000.000
66A81ALA0-0.026-0.01619.165-0.008-0.0080.0000.0000.0000.000
67A82VAL00.0040.00418.565-0.001-0.0010.0000.0000.0000.000
68A83VAL0-0.025-0.00320.1570.0000.0000.0000.0000.0000.000
69A84ASN00.0080.00520.704-0.006-0.0060.0000.0000.0000.000
70A85SER00.0030.00220.6680.0040.0040.0000.0000.0000.000
71A86GLU-1-0.874-0.93222.414-0.011-0.0110.0000.0000.0000.000
72A87ARG10.9160.94324.1380.0280.0280.0000.0000.0000.000
73A88ILE00.0470.04020.2590.0040.0040.0000.0000.0000.000
74A89ILE0-0.073-0.04121.7370.0020.0020.0000.0000.0000.000
75A90SER00.0950.04220.645-0.003-0.0030.0000.0000.0000.000
76A91HIS0-0.0020.00320.8220.0020.0020.0000.0000.0000.000
77A92SER0-0.010-0.01622.650-0.008-0.0080.0000.0000.0000.000
78A93MET0-0.047-0.02225.172-0.002-0.0020.0000.0000.0000.000
79A94PHE00.0550.04017.9200.0010.0010.0000.0000.0000.000
80A95ASN0-0.030-0.00221.670-0.003-0.0030.0000.0000.0000.000
81A96PRO0-0.005-0.01320.217-0.005-0.0050.0000.0000.0000.000
82A97ASP-1-0.906-0.93720.093-0.140-0.1400.0000.0000.0000.000
83A98THR0-0.050-0.06020.702-0.002-0.0020.0000.0000.0000.000
84A99TYR0-0.0190.00514.1760.0070.0070.0000.0000.0000.000
85A100LEU00.0190.02717.8500.0160.0160.0000.0000.0000.000
86A101ASN0-0.028-0.01820.0250.0020.0020.0000.0000.0000.000
87A102ASP-1-0.658-0.78114.198-0.200-0.2000.0000.0000.0000.000
88A103VAL0-0.047-0.00915.2850.0050.0050.0000.0000.0000.000
89A104ALA00.010-0.00516.509-0.005-0.0050.0000.0000.0000.000
90A105LEU0-0.0210.00217.0430.0100.0100.0000.0000.0000.000
91A106ILE00.0110.00916.882-0.011-0.0110.0000.0000.0000.000
92A107LYS10.8040.89919.7490.0160.0160.0000.0000.0000.000
93A108ILE00.0180.00719.026-0.011-0.0110.0000.0000.0000.000
94A109PRO00.0340.01122.8060.0060.0060.0000.0000.0000.000
95A111HIS0-0.085-0.07423.966-0.001-0.0010.0000.0000.0000.000
96A112VAL00.0090.02020.627-0.002-0.0020.0000.0000.0000.000
97A113GLU-1-0.906-0.94223.5340.0540.0540.0000.0000.0000.000
98A114TYR0-0.007-0.01120.4280.0040.0040.0000.0000.0000.000
99A115THR0-0.034-0.05221.111-0.002-0.0020.0000.0000.0000.000
100A116ASP-1-0.913-0.95121.0880.1200.1200.0000.0000.0000.000
101A117ASN0-0.074-0.05616.8120.0370.0370.0000.0000.0000.000
102A118ILE0-0.0230.01016.2160.0090.0090.0000.0000.0000.000
103A119GLN0-0.019-0.02916.662-0.013-0.0130.0000.0000.0000.000
104A120PRO0-0.0020.01816.2280.0070.0070.0000.0000.0000.000
105A121ILE0-0.016-0.00112.9080.0170.0170.0000.0000.0000.000
106A122ARG10.7630.85315.667-0.174-0.1740.0000.0000.0000.000
107A123LEU00.0370.01116.5590.0170.0170.0000.0000.0000.000
108A124PRO00.0160.00717.788-0.004-0.0040.0000.0000.0000.000
109A125SER0-0.007-0.01720.709-0.015-0.0150.0000.0000.0000.000
110A125GLY00.0160.00024.4780.0060.0060.0000.0000.0000.000
111A125GLU-1-0.817-0.92326.8270.0710.0710.0000.0000.0000.000
112A126GLU-1-0.814-0.84721.3660.1460.1460.0000.0000.0000.000
113A127LEU0-0.033-0.01922.1730.0070.0070.0000.0000.0000.000
114A128ASN0-0.021-0.01323.916-0.008-0.0080.0000.0000.0000.000
115A129ASN0-0.060-0.01821.2900.0060.0060.0000.0000.0000.000
116A130LYS10.8820.92420.366-0.087-0.0870.0000.0000.0000.000
117A131PHE00.002-0.01616.5460.0120.0120.0000.0000.0000.000
118A132GLU-1-0.801-0.89016.8380.1300.1300.0000.0000.0000.000
119A133ASN0-0.055-0.03717.094-0.003-0.0030.0000.0000.0000.000
120A134ILE0-0.0140.01014.935-0.004-0.0040.0000.0000.0000.000
121A135TRP00.0080.0079.9010.0190.0190.0000.0000.0000.000
122A136ALA0-0.0070.00210.063-0.053-0.0530.0000.0000.0000.000
123A137THR0-0.014-0.0216.3530.1380.1380.0000.0000.0000.000
124A138VAL0-0.0190.0112.390-1.264-0.5570.921-0.293-1.3350.004
125A139SER0-0.021-0.0322.709-0.4830.7470.796-0.687-1.338-0.003
126A140GLY0-0.009-0.0072.831-1.314-0.7460.7210.081-1.370-0.004
127A141TRP0-0.033-0.0253.149-0.0120.9880.166-0.330-0.836-0.003
128A142GLY0-0.0150.0063.0680.1090.6540.069-0.200-0.4150.001
129A143GLN0-0.017-0.0343.0471.0912.2620.450-0.651-0.971-0.004
130A144SER00.0570.0421.938-7.073-8.8187.249-2.931-2.573-0.025
131A145ASN0-0.019-0.0293.984-0.0330.1960.002-0.059-0.1720.000
132A146THR0-0.045-0.0196.9030.1860.1860.0000.0000.0000.000
133A147ASP-1-0.922-0.9457.922-0.267-0.2670.0000.0000.0000.000
134A152THR0-0.043-0.0577.0740.0210.0210.0000.0000.0000.000
135A153VAL00.0120.0168.8360.0270.0270.0000.0000.0000.000
136A154ILE0-0.046-0.0228.741-0.066-0.0660.0000.0000.0000.000
137A155LEU0-0.063-0.0105.1710.2660.2660.0000.0000.0000.000
138A156GLN00.0760.0332.439-1.558-0.5781.663-0.727-1.917-0.001
139A157TYR0-0.025-0.0342.646-2.632-0.9241.472-0.916-2.264-0.011
140A158THR00.0210.0052.432-1.543-0.3721.688-0.399-2.460-0.002
141A159TYR0-0.019-0.0023.869-0.434-0.2870.0050.004-0.1550.000
142A160ASN0-0.035-0.0365.5720.3680.3680.0000.0000.0000.000
143A161LEU0-0.0060.0128.600-0.059-0.0590.0000.0000.0000.000
144A162VAL00.0150.00812.325-0.016-0.0160.0000.0000.0000.000
145A163ILE0-0.039-0.00713.808-0.029-0.0290.0000.0000.0000.000
146A164ASP-1-0.825-0.90816.6210.0930.0930.0000.0000.0000.000
147A165ASN00.030-0.02018.9100.0130.0130.0000.0000.0000.000
148A166ASP-1-0.924-0.94620.2140.0310.0310.0000.0000.0000.000
149A167ARG10.8850.94517.132-0.140-0.1400.0000.0000.0000.000
150A168CYS0-0.036-0.03312.600-0.028-0.0280.0000.0000.0000.000
151A169ALA00.0450.00618.323-0.022-0.0220.0000.0000.0000.000
152A170GLN0-0.105-0.03720.961-0.011-0.0110.0000.0000.0000.000
153A170GLU-1-0.882-0.91617.355-0.033-0.0330.0000.0000.0000.000
154A171TYR0-0.024-0.03612.895-0.050-0.0500.0000.0000.0000.000
155A172PRO0-0.0130.00019.8060.0100.0100.0000.0000.0000.000
156A173PRO00.021-0.01822.4900.0040.0040.0000.0000.0000.000
157A174GLY0-0.018-0.00924.391-0.007-0.0070.0000.0000.0000.000
158A175ILE0-0.0010.01917.8410.0000.0000.0000.0000.0000.000
159A176ILE0-0.036-0.00316.5440.0040.0040.0000.0000.0000.000
160A177VAL00.0420.02219.7970.0020.0020.0000.0000.0000.000
161A178GLU-1-0.891-0.96420.4160.0210.0210.0000.0000.0000.000
162A179SER0-0.068-0.03420.1870.0140.0140.0000.0000.0000.000
163A180THR00.0170.02315.422-0.003-0.0030.0000.0000.0000.000
164A181ILE0-0.020-0.00713.0450.0080.0080.0000.0000.0000.000
165A183GLY00.0340.0289.9280.0300.0300.0000.0000.0000.000
166A184ASP-1-0.855-0.92210.8200.1480.1480.0000.0000.0000.000
167A185THR00.006-0.0137.4830.1240.1240.0000.0000.0000.000
168A186SER0-0.053-0.0479.277-0.073-0.0730.0000.0000.0000.000
169A186ASP-1-0.895-0.9349.6130.3310.3310.0000.0000.0000.000
170A187GLY0-0.0060.0008.8280.0060.0060.0000.0000.0000.000
171A188LYS10.8350.9254.809-0.763-0.7630.0000.0000.0000.000
172A189SER00.030-0.0083.736-0.2020.2250.003-0.114-0.3170.000
173A190PRO0-0.0010.0312.052-1.979-0.6915.891-3.594-3.585-0.016
174A191CYS0-0.064-0.0132.8640.4090.8800.1920.699-1.3620.003
175A192PHE00.049-0.0114.411-0.307-0.140-0.001-0.011-0.1550.000
176A193GLY00.0320.0315.268-0.474-0.4740.0000.0000.0000.000
177A194ASP-1-0.735-0.8621.832-12.951-16.59115.225-5.547-6.038-0.060
178A195SER0-0.053-0.0444.8940.5960.649-0.001-0.008-0.0440.000
179A196GLY00.003-0.0138.4050.0060.0060.0000.0000.0000.000
180A197GLY0-0.0080.0105.7820.0810.0810.0000.0000.0000.000
181A198PRO0-0.020-0.0045.9780.0630.0630.0000.0000.0000.000
182A199PHE00.0500.0306.1960.1980.1980.0000.0000.0000.000
183A200VAL00.007-0.0238.339-0.142-0.1420.0000.0000.0000.000
184A201LEU00.0120.02610.7120.0680.0680.0000.0000.0000.000
185A202SER00.035-0.01411.387-0.033-0.0330.0000.0000.0000.000
186A203ASP-1-0.895-0.92813.6230.2690.2690.0000.0000.0000.000
187A206LYS10.7990.88216.803-0.199-0.1990.0000.0000.0000.000
188A207ASN00.0140.00815.251-0.003-0.0030.0000.0000.0000.000
189A208LEU0-0.059-0.02715.513-0.028-0.0280.0000.0000.0000.000
190A209LEU00.0310.02510.8370.0420.0420.0000.0000.0000.000
191A210ILE0-0.038-0.03112.410-0.043-0.0430.0000.0000.0000.000
192A211GLY0-0.010-0.01911.643-0.036-0.0360.0000.0000.0000.000
193A212VAL0-0.0210.0079.8220.0410.0410.0000.0000.0000.000
194A213VAL0-0.0170.0014.8920.0180.0180.0000.0000.0000.000
195A214SER0-0.053-0.0488.340-0.108-0.1080.0000.0000.0000.000
196A215PHE00.0330.00310.806-0.072-0.0720.0000.0000.0000.000
197A216VAL00.0480.0327.2870.0910.0910.0000.0000.0000.000
198A217SER00.0630.03210.3200.0190.0190.0000.0000.0000.000
199A217GLY00.0190.00912.738-0.076-0.0760.0000.0000.0000.000
200A218ALA0-0.076-0.04114.540-0.021-0.0210.0000.0000.0000.000
201A219GLY00.0190.00911.168-0.016-0.0160.0000.0000.0000.000
202A221GLU-1-0.862-0.9257.547-0.748-0.7480.0000.0000.0000.000
203A222SER0-0.075-0.0509.7820.1340.1340.0000.0000.0000.000
204A223GLY00.0140.01911.0660.0430.0430.0000.0000.0000.000
205A224LYS10.7510.87312.2660.1310.1310.0000.0000.0000.000
206A225PRO00.0290.01911.2670.0120.0120.0000.0000.0000.000
207A226VAL0-0.0060.0256.755-0.092-0.0920.0000.0000.0000.000
208A227GLY00.0440.02110.0230.0870.0870.0000.0000.0000.000
209A228PHE0-0.016-0.0196.577-0.060-0.0600.0000.0000.0000.000
210A229SER0-0.002-0.01011.670-0.011-0.0110.0000.0000.0000.000
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